Growth-chamber mesocosm soil, live soil, unoiled, t=0 baseline soil, replicate 2
Growth-chamber mesocosm experiment testing the effect of weathered Deepwater Horizon oil and soil autoclaving on the salt marsh soil microbiome. Full-factorial design, 3 sequenced replicates per cell. 16S rRNA V4 and fungal ITS1 amplicons were generated from this same DNA extract. This is an experimental sample, not a field sample.
collection_date
2018-05-04
depth
0-0.1 m
elev
3 m
env_broad_scale
laboratory environment [ENVO:01001405]
env_local_scale
microcosm [ENVO:01000621]
env_medium
soil [ENVO:00001998]
geo_loc_name
USA: Louisiana, New Orleans
lat_lon
29.9404 N 90.1215 W
collection_method
subsampled from homogenized bulk soil into 50 mL conical tube
isolation_source
Source material: salt marsh soil collected 2018-05-02 from the 0-0.1 m horizon at Bay Jimmy, Louisiana, USA (29.440446 N 89.885863 W), sieved through 6.35 mm (1/4 inch) hardware cloth and homogenized, so no sample retains depth stratification; field-moist (live) salt marsh soil; no oil added. EXPERIMENTAL SAMPLE, NOT A FIELD SAMPLE: subsampled from the homogenized bulk soil at mesocosm assembly (t=0) at Tulane University, New Orleans, Louisiana, USA, before planting and before any growth-chamber incubation. Frozen at -20 C.
misc_param
soil treatment:live;oil treatment:no;experiment phase:baseline
pool_dna_extracts
No
samp_collect_device
50 mL conical tube
samp_mat_process
Bulk source soil sieved through 6.35 mm (1/4 inch) hardware cloth on a wooden frame, and homogenized, before use; autoclaved fraction processed at 121 C for 60 min, rested 6 h, mixed and autoclaved again. Sampled soil placed on dry ice within 5 min of collection and stored at -20 C until extraction. DNA extracted from 0.25 g soil with the Qiagen DNeasy PowerSoil kit (cat# 12888) per manufacturer protocol.
samp_size
50 mL
samp_vol_we_dna_ext
0.25 g
soil_type
salt marsh soil
source_material_id
SF1_LN2
store_cond
-20 C
soil_treatment
live
oil_treatment
no
experiment_phase
baseline
mesocosm_id
not applicable
experimental_block
not applicable
days_incubated
0
BioSampleModel
MIMARKS.survey
BioSampleModel
MIGS/MIMS/MIMARKS.soil